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Published online 11 March 2004

Nucleic Acids Research, 2004, Vol. 32, No. 5 1666-1677
© 2004 Oxford University Press

RNA conformational classes

Bohdan Schneider*, Zdenek Morávek1 and Helen M. Berman2

Center for Complex Molecular Systems and Biomolecules and Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo n.2, CZ-16610 Prague, Czech Republic, 1 Faculty of Mathematics and Physics, Charles University, Ke Karlovu 2, Prague, Czech Republic and 2 Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, Piscataway, NJ 08854, USA

*To whom correspondence should be addressed. Tel: +420 728 303 566; Fax: +420 224 310 090; Email: bohdan{at}uochb.cas.cz

RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron maps, followed by clustering of the preferred combinations of torsion angles were performed on this dataset. Eighteen non-A-type conformations and 14 A-RNA related conformations were discovered and their torsion angles were determined; their Cartesian coordinates are available.


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